Coot is a powerful macromolecular model-building tool for analysing X-ray data and models (i.e. proteins, ligands, RNA and DNA). There are many tools for model manipulation and building, such as minimization, molecular superposition, fragment rotation/translations, rotamer-fitting, de novo building and refinement.

Coot is used by scientists using X-ray crystallography for analysis of proteins, electron density maps, protein interactions and drug design.